The lipopolysaccharide (LPS) signaling pathway has been analyzed using combination of biochemical and genetic methods. However, not all of the proteins that participate in LPS recognition have been identified. In order to find more of them, several inbred strains of mice were evaluated on their LPS response and genetic basis of the differences in this response was examined. Among them, BALB/C and C3H/HeN strains differ significantly in their response to LPS. To further determine the relationship between TLR4 LPS response, (BALB/C x C3H/HeN) F2 intercross mice were analyzed on their LPS response and genotyped for TLR4 locus. These data show that although there is functional polymorphism in TLR4 observed between BALB/C and C3H/HeN mice, additional genes are clearly involved in LPS response. In order to map these genes, the panel of F2 mice was expanded and subjected to genome wide screening with all progeny genotyped for TLR4 locus. Genetic analysis of 80 meioses revealed that hyporesponse of BALB/C mice to LPS is linked to loci on chromosomes 6 and 17. To further characterize candidates and to improve resolution of genetic mapping, two congenic strains were constructed: one with BALB/C allele of TLR4 on C3H/HeN background and another - with HeN allele of TLR4 on BALB/C background. These strains were further analyzed to determine the level of their response to LPS. Two new loci, termed Lpml and Lpm2, may be assumed to contribute to the LPS response. The elucidation of Lpml and Lpm2 will represent an important advance, in that many genes that are known to contribute to complex traits can be identified by such approach. Similar strategy was employed for analysis of intercross response to peptidoglycan in F2 intercross animals. Elucidation of a precise mechanism of anti-bacterial response in a mouse model will undoubtedly contribute to the studies of host resistance to infectious diseases in humans.